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SingleNetworkMinimizable Class Reference

#include <SingleNetworkMinimizable.h>

Inheritance diagram for SingleNetworkMinimizable:

[legend]Collaboration diagram for SingleNetworkMinimizable:

Public Methods
	SingleNetworkMinimizable ()
virtual	~SingleNetworkMinimizable ()
	SingleNetworkMinimizable (Experiment experiment, CReactionMover reactionMover, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight, int nCells=1)
void	Initialize (Experiment experiment, CReactionMover reactionMover, int nCells, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight)
Experiment *	GetExperiment ()
CellAverageObserver *	GetCellObserver ()
double	GetParameter (int parIndex)
int	GetNParameters ()
double	ComputeResiduals (double *parameters)
virtual double	ComputeES (double *parameters, double T)
virtual double	F (double *parameters, double T)
virtual double	F0 (double *parameters, double T)
	SingleNetworkMinimizable ()
	SingleNetworkMinimizable (Experiment experiment, CReactionMover reactionMover, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight, int nCells=1)
void	Initialize (Experiment experiment, CReactionMover reactionMover, int nCells, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight)
virtual	~SingleNetworkMinimizable ()
Experiment *	GetExperiment ()
CellAverageObserver *	GetCellObserver ()
int	GetNCells ()
bool	GetRateConstantsOptimizable () const
bool	GetInitialChemConcOptimizable () const
bool	GetLogsInObjectiveFunction () const
double	GetTimeSeriesWeight () const
double	GetRateConstantsWeight () const
double	GetInitialChemConcWeight () const
void	SetTimeSeriesWeight (double timeSeriesWeight)
void	SetRateConstantsWeight (double rateConstantsWeight)
void	SetInitialChemConcWeight (double initialChemConcWeight)
double	GetParameter (int parIndex)
int	GetNParameters ()
double	ComputeResiduals (double *parameters)
CConversionFactor *	GetConversionFactor (int factorIndex)
virtual double	ComputeES (double *parameters, double T)
virtual double	EntropyShift (double T)
virtual double	F (double *parameters, double T)
virtual double	F0 (double *parameters, double T)
int	GetNBFactors ()
Private Attributes
Experiment *	experiment
CReactionMover *	reactionMover
CellAverageObserver *	cellObserver
double *	initialNetworkData
double *	currentNetworkData
bool	rateConstantsOptimizable
bool	initialChemConcOptimizable
bool	logsInObjectiveFunction
Experiment *	experiment
CReactionMover *	reactionMover
CellAverageObserver *	cellObserver
int	nCells
double	timeSeriesWeight
double	rateConstantsWeight
double	initialChemConcWeight
double *	initialNetworkData
double *	currentNetworkData
std::vector< CConversionFactor * >	m_pConversionFactors
int	m_iNBFactors

Constructor & Destructor Documentation

SingleNetworkMinimizable::SingleNetworkMinimizable ( )

Definition at line 11 of file SingleNetworkMinimizable.cpp.

SingleNetworkMinimizable::~SingleNetworkMinimizable ( ) [virtual]

Definition at line 21 of file SingleNetworkMinimizable.cpp.
References cellObserver, currentNetworkData, Subject::Detach, initialNetworkData, m_pConversionFactors, and reactionMover.

SingleNetworkMinimizable::SingleNetworkMinimizable ( Experiment * experiment,

CReactionMover * reactionMover,

bool rateConstantsOptimizable,

bool initialChemConcOptimizable,

bool logsInObjectiveFunction,

double timeSeriesWeight,

double rateConstantsWeight,

double initialChemConcWeight,

int nCells = 1

)

Definition at line 16 of file SingleNetworkMinimizable.cpp.
References initialChemConcOptimizable, initialChemConcWeight, Initialize, logsInObjectiveFunction, nCells, rateConstantsOptimizable, rateConstantsWeight, and timeSeriesWeight.

SingleNetworkMinimizable::SingleNetworkMinimizable ( )

virtual SingleNetworkMinimizable::~SingleNetworkMinimizable ( ) [virtual]

Member Function Documentation

virtual double SingleNetworkMinimizable::ComputeES ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.

double SingleNetworkMinimizable::ComputeES ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.
Definition at line 106 of file SingleNetworkMinimizable.cpp.
References ComputeResiduals, EntropyShift, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

double SingleNetworkMinimizable::ComputeResiduals ( double * parameters ) [virtual]

Implements NetworkMinimizable.

double SingleNetworkMinimizable::ComputeResiduals ( double * parameters ) [virtual]

Implements NetworkMinimizable.
Definition at line 135 of file SingleNetworkMinimizable.cpp.
References cellObserver, ReactionNetwork::ChemicalReset, currentNetworkData, experiment, CellAverageObserver::GetAverageConcentration, ReactionNetwork::GetChemical, Experiment::GetChemicalTimeSeriesData, Chemical::GetErrorInInitialAmount, RateConstant::GetErrorInInitialValue, Experiment::GetForcingData, CForcingData::GetForcingVector, ChemicalTimeSeriesData::GetLatestDataTime, CForcingData::GetLatestForcingTime, ReactionNetwork::GetNumberOfChemicals, ReactionNetwork::GetNumberOfRateConstants, ReactionNetwork::GetRateConstant, Experiment::GetReactionNetwork, ChemicalTimeSeriesData::GetTimeSeries, ChemicalTimeSeriesData::GetTimeVector, initialChemConcOptimizable, initialChemConcWeight, initialNetworkData, Minimizable::m_dEntropyLastComputed, m_iNBFactors, m_pConversionFactors, CReactionMover::Move, nCells, Subject::Notify, ReactionNetwork::RateConstantReset, rateConstantsOptimizable, rateConstantsWeight, reactionMover, CReactionMover::ResetStepStatistics, NLLSMinimizable::residuals, Chemical::SetAmount, RateConstant::SetRateConstant, stop, timeSeriesWeight, and CellAverageObserver::ZeroConcentrations.
Referenced by ComputeES, F, and F0.

double SingleNetworkMinimizable::EntropyShift ( double T ) [virtual]

Reimplemented from NetworkMinimizable.
Definition at line 109 of file SingleNetworkMinimizableOLD.cpp.
References m_iNBFactors.
Referenced by ComputeES, and F0.

virtual double SingleNetworkMinimizable::F ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.

double SingleNetworkMinimizable::F ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.
Definition at line 119 of file SingleNetworkMinimizable.cpp.
References ComputeResiduals, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

virtual double SingleNetworkMinimizable::F0 ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.

double SingleNetworkMinimizable::F0 ( double * parameters,

double T

) [virtual]

Implements NetworkMinimizable.
Definition at line 127 of file SingleNetworkMinimizable.cpp.
References ComputeResiduals, EntropyShift, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

CellAverageObserver* SingleNetworkMinimizable::GetCellObserver ( ) [inline]

Definition at line 33 of file SingleNetworkMinimizableOLD.h.
References cellObserver.

CellAverageObserver* SingleNetworkMinimizable::GetCellObserver ( ) [inline]

Definition at line 34 of file SingleNetworkMinimizable.h.
References cellObserver.
Referenced by GnuPlotterTrajectoryObserver::Update, GnuPlotterTimeSeriesObserver::Update, and GnuPlotterEnsembleDataDirectorObserver::Update.

CConversionFactor* SingleNetworkMinimizable::GetConversionFactor ( int factorIndex ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 49 of file SingleNetworkMinimizableOLD.h.
References m_pConversionFactors.
Referenced by GnuPlotterTimeSeriesObserver::Update.

Experiment* SingleNetworkMinimizable::GetExperiment ( ) [inline, virtual]

Reimplemented from NetworkMinimizable.
Definition at line 32 of file SingleNetworkMinimizableOLD.h.

Experiment* SingleNetworkMinimizable::GetExperiment ( ) [inline, virtual]

Reimplemented from NetworkMinimizable.
Definition at line 33 of file SingleNetworkMinimizable.h.
Referenced by GnuPlotterTrajectoryObserver::Update, GnuPlotterTimeSeriesObserver::Update, and GnuPlotterEnsembleDataDirectorObserver::Update.

bool SingleNetworkMinimizable::GetInitialChemConcOptimizable ( ) const [inline]

Reimplemented from NetworkMinimizable.
Definition at line 36 of file SingleNetworkMinimizableOLD.h.
References initialChemConcOptimizable.

double SingleNetworkMinimizable::GetInitialChemConcWeight ( ) const [inline]

Definition at line 40 of file SingleNetworkMinimizableOLD.h.
References initialChemConcWeight.

bool SingleNetworkMinimizable::GetLogsInObjectiveFunction ( ) const [inline]

Reimplemented from NetworkMinimizable.
Definition at line 37 of file SingleNetworkMinimizableOLD.h.
References logsInObjectiveFunction.

int SingleNetworkMinimizable::GetNBFactors ( ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 54 of file SingleNetworkMinimizableOLD.h.
References m_iNBFactors.

int SingleNetworkMinimizable::GetNCells ( ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 34 of file SingleNetworkMinimizableOLD.h.
References nCells.

int SingleNetworkMinimizable::GetNParameters ( ) [virtual]

Implements NetworkMinimizable.

int SingleNetworkMinimizable::GetNParameters ( ) [virtual]

Implements NetworkMinimizable.
Definition at line 411 of file SingleNetworkMinimizable.cpp.
References experiment, ReactionNetwork::GetNumberOfChemicals, ReactionNetwork::GetNumberOfRateConstants, Experiment::GetReactionNetwork, initialChemConcOptimizable, and rateConstantsOptimizable.
Referenced by GetParameter.

double SingleNetworkMinimizable::GetParameter ( int parIndex ) [virtual]

Implements NetworkMinimizable.

double SingleNetworkMinimizable::GetParameter ( int parIndex ) [virtual]

Implements NetworkMinimizable.
Definition at line 437 of file SingleNetworkMinimizable.cpp.
References currentNetworkData, and GetNParameters.

bool SingleNetworkMinimizable::GetRateConstantsOptimizable ( ) const [inline]

Reimplemented from NetworkMinimizable.
Definition at line 35 of file SingleNetworkMinimizableOLD.h.
References rateConstantsOptimizable.

double SingleNetworkMinimizable::GetRateConstantsWeight ( ) const [inline]

Definition at line 39 of file SingleNetworkMinimizableOLD.h.
References rateConstantsWeight.

double SingleNetworkMinimizable::GetTimeSeriesWeight ( ) const [inline]

Definition at line 38 of file SingleNetworkMinimizableOLD.h.
References timeSeriesWeight.

void SingleNetworkMinimizable::Initialize ( Experiment * experiment,

CReactionMover * reactionMover,

int nCells,

bool rateConstantsOptimizable,

bool initialChemConcOptimizable,

bool logsInObjectiveFunction,

double timeSeriesWeight,

double rateConstantsWeight,

double initialChemConcWeight

) [virtual]

Reimplemented from NetworkMinimizable.
Definition at line 38 of file SingleNetworkMinimizable.cpp.
References NLLSMinimizable::Allocate, Subject::Attach, cellObserver, currentNetworkData, ReactionNetwork::GetChemical, Experiment::GetChemicalTimeSeriesData, Chemical::GetInitialAmount, RateConstant::GetInitialValue, ChemicalTimeSeriesData::GetLatestDataTime, ChemicalTimeSeriesData::GetNDataPoints, ReactionNetwork::GetNumberOfChemicals, ReactionNetwork::GetNumberOfRateConstants, ReactionNetwork::GetRateConstant, Experiment::GetReactionNetwork, ChemicalTimeSeriesData::GetTimeSeries, initialChemConcOptimizable, initialChemConcWeight, initialNetworkData, logsInObjectiveFunction, m_iNBFactors, m_pConversionFactors, nCells, rateConstantsOptimizable, rateConstantsWeight, Experiment::ReadData, Experiment::ReadForcingData, SetInitialChemConcWeight, SetRateConstantsWeight, SetTimeSeriesWeight, and timeSeriesWeight.
Referenced by SingleNetworkMinimizable.

void SingleNetworkMinimizable::SetInitialChemConcWeight ( double initialChemConcWeight ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 43 of file SingleNetworkMinimizableOLD.h.
References initialChemConcWeight.
Referenced by Initialize.

void SingleNetworkMinimizable::SetRateConstantsWeight ( double rateConstantsWeight ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 42 of file SingleNetworkMinimizableOLD.h.
References rateConstantsWeight.
Referenced by Initialize.

void SingleNetworkMinimizable::SetTimeSeriesWeight ( double timeSeriesWeight ) [inline]

Reimplemented from NetworkMinimizable.
Definition at line 41 of file SingleNetworkMinimizableOLD.h.
References timeSeriesWeight.
Referenced by Initialize.

Member Data Documentation

CellAverageObserver* SingleNetworkMinimizable::cellObserver [private]

Definition at line 61 of file SingleNetworkMinimizableOLD.h.

CellAverageObserver* SingleNetworkMinimizable::cellObserver [private]

Definition at line 47 of file SingleNetworkMinimizable.h.
Referenced by ComputeResiduals, GetCellObserver, Initialize, and ~SingleNetworkMinimizable.

double* SingleNetworkMinimizable::currentNetworkData [private]

Definition at line 67 of file SingleNetworkMinimizableOLD.h.

double* SingleNetworkMinimizable::currentNetworkData [private]

Definition at line 49 of file SingleNetworkMinimizable.h.
Referenced by ComputeResiduals, GetParameter, Initialize, and ~SingleNetworkMinimizable.

Experiment* SingleNetworkMinimizable::experiment [private]

Definition at line 59 of file SingleNetworkMinimizableOLD.h.

Experiment* SingleNetworkMinimizable::experiment [private]

Definition at line 45 of file SingleNetworkMinimizable.h.
Referenced by ComputeResiduals, and GetNParameters.

bool SingleNetworkMinimizable::initialChemConcOptimizable [private]

Reimplemented from NetworkMinimizable.
Definition at line 57 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetInitialChemConcOptimizable, GetNParameters, Initialize, and SingleNetworkMinimizable.

double SingleNetworkMinimizable::initialChemConcWeight [private]

Reimplemented from NetworkMinimizable.
Definition at line 65 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetInitialChemConcWeight, Initialize, SetInitialChemConcWeight, and SingleNetworkMinimizable.

double* SingleNetworkMinimizable::initialNetworkData [private]

Definition at line 66 of file SingleNetworkMinimizableOLD.h.

double* SingleNetworkMinimizable::initialNetworkData [private]

Definition at line 48 of file SingleNetworkMinimizable.h.
Referenced by ComputeResiduals, Initialize, and ~SingleNetworkMinimizable.

bool SingleNetworkMinimizable::logsInObjectiveFunction [private]

Reimplemented from NetworkMinimizable.
Definition at line 58 of file SingleNetworkMinimizableOLD.h.
Referenced by GetLogsInObjectiveFunction, Initialize, and SingleNetworkMinimizable.

int SingleNetworkMinimizable::m_iNBFactors [private]

Reimplemented from NetworkMinimizable.
Definition at line 70 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, EntropyShift, GetNBFactors, and Initialize.

std::vector<CConversionFactor *> SingleNetworkMinimizable::m_pConversionFactors [private]

Reimplemented from NetworkMinimizable.
Definition at line 68 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetConversionFactor, Initialize, and ~SingleNetworkMinimizable.

int SingleNetworkMinimizable::nCells [private]

Reimplemented from NetworkMinimizable.
Definition at line 62 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetNCells, Initialize, and SingleNetworkMinimizable.

bool SingleNetworkMinimizable::rateConstantsOptimizable [private]

Reimplemented from NetworkMinimizable.
Definition at line 56 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetNParameters, GetRateConstantsOptimizable, Initialize, and SingleNetworkMinimizable.

double SingleNetworkMinimizable::rateConstantsWeight [private]

Reimplemented from NetworkMinimizable.
Definition at line 64 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetRateConstantsWeight, Initialize, SetRateConstantsWeight, and SingleNetworkMinimizable.

CReactionMover* SingleNetworkMinimizable::reactionMover [private]

Definition at line 60 of file SingleNetworkMinimizableOLD.h.

CReactionMover* SingleNetworkMinimizable::reactionMover [private]

Definition at line 46 of file SingleNetworkMinimizable.h.
Referenced by ComputeResiduals, and ~SingleNetworkMinimizable.

double SingleNetworkMinimizable::timeSeriesWeight [private]

Reimplemented from NetworkMinimizable.
Definition at line 63 of file SingleNetworkMinimizableOLD.h.
Referenced by ComputeResiduals, GetTimeSeriesWeight, Initialize, SetTimeSeriesWeight, and SingleNetworkMinimizable.

The documentation for this class was generated from the following files:

Generated on Mon Nov 3 10:08:11 2003 by

SingleNetworkMinimizable Class Reference

Public Methods

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation